Following the death of the Rev Shaw the congregation of Boardmills County Down called Mr. John Downes, who was born in Falkirk, Stirlingshire Scotland, on 24th July, 1802. He received his education at the local grammar school and at the University of Glasgow. As he had also received calls from Longridge and Kennoway in Scotland the matter was referred to the Synod, which decided on the 10th May, 1826, that he should accept the call to Boardmills County Down and appointed his ordination to be gone about in due form. He was ordained in the following year.
The Rev. Downes was twice married. His first wife, whom he married on the 17th October, 1833, was Mary, eldest daughter of David Jamison of Prospect. She died on the 3rd September, 1840, aged 26
The Rev. Downes was a man of great versatility and talent, and his sermons, extending often to an hour and a half in length, were characterised by great vigour and poetic beauty. During his pastorate in Boardmills he published a sermon "The God of Bethel."
He then married, on 11th October, 1842, Martha, third daughter of John Gilmore, Ballycarnagannon, 
This step did not meet with the approval of some members of the congregation, the result being that several, who had thought it a duty to travel some miles on the Sabbath to worship at Boardmills, connected themselves with other communions or joined congregations more convenient to their homes. This weakening of the congregation, plus the fact that a few years later he became involved in a theological dispute between the Rev. George Hay Shanks of First Boardmills and the Rev. Thomas Clugston of Killaney Secession Church, encouraged the Rev. Downes to consider leaving Second Boardmills, as it was known since it joined the General Assembly. In1851, Mr. Downes and the Boardmills congregation had applied to the Belfast Presbytery to be received into the General Assembly A year later, on the 7th July, 1852, the General Assembly sanctioned the action of the Presbytery in receiving them.
He received a call to Hobart, Tasmania, in circumstances highly honourable to himself. A Boardmills man whom Mr. Downes had educated when orphaned influenced a call to that distant field. The call was accompanied by a cheque for £400 to bring him and his family over. Mr. Downes accepted the call, and resigned his congregation on the 7th August 1855. Accompanied by his wife Martha and seven children he sailed in "The Champion of the Seas" for Hobart, where he arrived in October, 1855.